2WQY

Remodelling of carboxin binding to the Q-site of avian respiratory complex II

PDB DOI: https://doi.org/10.2210/pdb2WQY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Gallus gallus
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2009-08-27 Released: 2010-08-25
Deposition Author(s): Ruprecht, J., Iwata, S., Cecchini, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.223
R-Value Work: 0.184
R-Value Observed: 0.186

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2FBW

Literature

Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II

Ruprecht, J., Iwata, S., Cecchini, G.

To be published.

Macromolecule Content

Total Structure Weight: 254.43 kDa
Atom Count: 19,490
Modelled Residue Count: 2,185
Deposited Residue Count: 2,234
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT	A, E [auth N]	621	Gallus gallus	Mutation(s): 0 EC: 1.3.5.1 (PDB Primary Data), 1.1.5 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q9YHT1 (Gallus gallus) Explore Q9YHT1 Go to UniProtKB: Q9YHT1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9YHT1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE IP SUBUNIT	B, F [auth O]	252	Gallus gallus	Mutation(s): 0 EC: 1.3.5.1 (PDB Primary Data), 1.1.5 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q9YHT2 (Gallus gallus) Explore Q9YHT2 Go to UniProtKB: Q9YHT2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9YHT2
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT	C, G [auth P]	141	Gallus gallus	Mutation(s): 0 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for D0VWW3 (Gallus gallus) Explore D0VWW3 Go to UniProtKB: D0VWW3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VWW3
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT	D, H [auth Q]	103	Gallus gallus	Mutation(s): 0 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for Q5ZIS0 (Gallus gallus) Explore Q5ZIS0 Go to UniProtKB: Q5ZIS0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZIS0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 13 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain AC [auth N] SDF format, chain M [auth A] MOL2 format, chain AC [auth N] MOL2 format, chain M [auth A] mmCIF format, chain AC [auth N] mmCIF format, chain M [auth A]	AC [auth N], M [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain AC [auth N] Focus chain M [auth A] Interactions & Density Focus chain AC [auth N] Focus chain M [auth A]
PEE Query on PEE Download Ideal Coordinates CCD File SDF format, chain PB [auth D] SDF format, chain TD [auth Q] MOL2 format, chain PB [auth D] MOL2 format, chain TD [auth Q] mmCIF format, chain PB [auth D] mmCIF format, chain TD [auth Q]	PB [auth D], TD [auth Q]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain PB [auth D] Focus chain TD [auth Q] Interactions & Density Focus chain PB [auth D] Focus chain TD [auth Q]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain XA [auth C] SDF format, chain ID [auth P] MOL2 format, chain XA [auth C] MOL2 format, chain ID [auth P] mmCIF format, chain XA [auth C] mmCIF format, chain ID [auth P]	ID [auth P], XA [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain ID [auth P] Focus chain XA [auth C] Interactions & Density Focus chain ID [auth P] Focus chain XA [auth C]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain BD [auth O] SDF format, chain OA [auth B] MOL2 format, chain BD [auth O] MOL2 format, chain OA [auth B] mmCIF format, chain BD [auth O] mmCIF format, chain OA [auth B]	BD [auth O], OA [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain BD [auth O] Focus chain OA [auth B] Interactions & Density Focus chain BD [auth O] Focus chain OA [auth B]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain CD [auth O] SDF format, chain PA [auth B] MOL2 format, chain CD [auth O] MOL2 format, chain PA [auth B] mmCIF format, chain CD [auth O] mmCIF format, chain PA [auth B]	CD [auth O], PA [auth B]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain CD [auth O] Focus chain PA [auth B] Interactions & Density Focus chain CD [auth O] Focus chain PA [auth B]
BHG Query on BHG Download Ideal Coordinates CCD File SDF format, chain KD [auth P] SDF format, chain WA [auth C] MOL2 format, chain KD [auth P] MOL2 format, chain WA [auth C] mmCIF format, chain KD [auth P] mmCIF format, chain WA [auth C]	KD [auth P], WA [auth C]	hexyl beta-D-galactopyranoside C₁₂ H₂₄ O₆ JVAZJLFFSJARQM-YBXAARCKSA-N		Interactions Focus chain KD [auth P] Focus chain WA [auth C] Interactions & Density Focus chain KD [auth P] Focus chain WA [auth C]
CBE Query on CBE Download Ideal Coordinates CCD File SDF format, chain JD [auth P] SDF format, chain YA [auth C] MOL2 format, chain JD [auth P] MOL2 format, chain YA [auth C] mmCIF format, chain JD [auth P] mmCIF format, chain YA [auth C]	JD [auth P], YA [auth C]	2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE C₁₂ H₁₃ N O₂ S GYSSRZJIHXQEHQ-UHFFFAOYSA-N		Interactions Focus chain JD [auth P] Focus chain YA [auth C] Interactions & Density Focus chain JD [auth P] Focus chain YA [auth C]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain AD [auth O] SDF format, chain NA [auth B] MOL2 format, chain AD [auth O] MOL2 format, chain NA [auth B] mmCIF format, chain AD [auth O] mmCIF format, chain NA [auth B]	AD [auth O], NA [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain AD [auth O] Focus chain NA [auth B] Interactions & Density Focus chain AD [auth O] Focus chain NA [auth B]
OAA Query on OAA Download Ideal Coordinates CCD File SDF format, chain BC [auth N] SDF format, chain N [auth A] MOL2 format, chain BC [auth N] MOL2 format, chain N [auth A] mmCIF format, chain BC [auth N] mmCIF format, chain N [auth A]	BC [auth N], N [auth A]	OXALOACETATE ION C₄ H₃ O₅ KHPXUQMNIQBQEV-UHFFFAOYSA-M		Interactions Focus chain BC [auth N] Focus chain N [auth A] Interactions & Density Focus chain BC [auth N] Focus chain N [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain LD [auth P] SDF format, chain OB [auth C] SDF format, chain HD [auth O] SDF format, chain VA [auth B] MOL2 format, chain LD [auth P] MOL2 format, chain OB [auth C] MOL2 format, chain HD [auth O] MOL2 format, chain VA [auth B] mmCIF format, chain LD [auth P] mmCIF format, chain OB [auth C] mmCIF format, chain HD [auth O] mmCIF format, chain VA [auth B]	HD [auth O], LD [auth P], OB [auth C], VA [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain HD [auth O] Focus chain LD [auth P] Focus chain OB [auth C] Focus chain VA [auth B] Interactions & Density Focus chain HD [auth O] Focus chain LD [auth P] Focus chain OB [auth C] Focus chain VA [auth B]
AZI Query on AZI Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain K [auth A] SDF format, chain XC [auth O] SDF format, chain ZB [auth N] MOL2 format, chain HA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain XC [auth O] MOL2 format, chain ZB [auth N] mmCIF format, chain HA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain XC [auth O] mmCIF format, chain ZB [auth N]	HA [auth B], K [auth A], XC [auth O], ZB [auth N]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain K [auth A] Focus chain XC [auth O] Focus chain ZB [auth N] Interactions & Density Focus chain HA [auth B] Focus chain K [auth A] Focus chain XC [auth O] Focus chain ZB [auth N]
UNL Query on UNL Download Ideal Coordinates CCD File	AA [auth A] AB [auth C] BA [auth A] BB [auth C] CA [auth A] AA [auth A], AB [auth C], BA [auth A], BB [auth C], CA [auth A], CB [auth C], CC [auth N], DA [auth A], DB [auth C], DC [auth N], DD [auth O], EA [auth A], EB [auth C], EC [auth N], ED [auth O], FA [auth A], FB [auth C], FC [auth N], FD [auth O], GA [auth A], GB [auth C], GC [auth N], GD [auth O], HB [auth C], HC [auth N], I [auth A], IA [auth B], IB [auth C], IC [auth N], J [auth A], JA [auth B], JB [auth C], JC [auth N], KA [auth B], KB [auth C], KC [auth N], LA [auth B], LB [auth C], LC [auth N], MA [auth B], MB [auth C], MC [auth N], MD [auth P], NB [auth C], NC [auth N], ND [auth P], O [auth A], OC [auth N], OD [auth P], P [auth A], PC [auth N], PD [auth P], Q [auth A], QA [auth B], QB [auth D], QC [auth N], QD [auth P], R [auth A], RA [auth B], RB [auth D], RC [auth N], RD [auth P], S [auth A], SA [auth B], SB [auth D], SC [auth N], SD [auth P], T [auth A], TA [auth B], TB [auth D], TC [auth N], U [auth A], UA [auth B], UB [auth D], UC [auth N], UD [auth Q], V [auth A], VB [auth D], VC [auth N], VD [auth Q], W [auth A], WB [auth D], WC [auth N], WD [auth Q], X [auth A], XB [auth D], XD [auth Q], Y [auth A], YB [auth D], YC [auth O], YD [auth Q], Z [auth A], ZA [auth C], ZC [auth O], ZD [auth Q]	Unknown ligand NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain CC [auth N] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain DC [auth N] Focus chain DD [auth O] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain EC [auth N] Focus chain ED [auth O] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain FC [auth N] Focus chain FD [auth O] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain GC [auth N] Focus chain GD [auth O] Focus chain HB [auth C] Focus chain HC [auth N] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain IC [auth N] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain JC [auth N] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth N] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain LC [auth N] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth N] Focus chain MD [auth P] Focus chain NB [auth C] Focus chain NC [auth N] Focus chain ND [auth P] Focus chain O [auth A] Focus chain OC [auth N] Focus chain OD [auth P] Focus chain P [auth A] Focus chain PC [auth N] Focus chain PD [auth P] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain QC [auth N] Focus chain QD [auth P] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain RC [auth N] Focus chain RD [auth P] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth D] Focus chain SC [auth N] Focus chain SD [auth P] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth D] Focus chain TC [auth N] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth D] Focus chain UC [auth N] Focus chain UD [auth Q] Focus chain V [auth A] Focus chain VB [auth D] Focus chain VC [auth N] Focus chain VD [auth Q] Focus chain W [auth A] Focus chain WB [auth D] Focus chain WC [auth N] Focus chain WD [auth Q] Focus chain X [auth A] Focus chain XB [auth D] Focus chain XD [auth Q] Focus chain Y [auth A] Focus chain YB [auth D] Focus chain YC [auth O] Focus chain YD [auth Q] Focus chain Z [auth A] Focus chain ZA [auth C] Focus chain ZC [auth O] Focus chain ZD [auth Q] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain CC [auth N] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain DC [auth N] Focus chain DD [auth O] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain EC [auth N] Focus chain ED [auth O] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain FC [auth N] Focus chain FD [auth O] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain GC [auth N] Focus chain GD [auth O] Focus chain HB [auth C] Focus chain HC [auth N] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain IC [auth N] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain JC [auth N] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth N] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain LC [auth N] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth N] Focus chain MD [auth P] Focus chain NB [auth C] Focus chain NC [auth N] Focus chain ND [auth P] Focus chain O [auth A] Focus chain OC [auth N] Focus chain OD [auth P] Focus chain P [auth A] Focus chain PC [auth N] Focus chain PD [auth P] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain QC [auth N] Focus chain QD [auth P] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain RC [auth N] Focus chain RD [auth P] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth D] Focus chain SC [auth N] Focus chain SD [auth P] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth D] Focus chain TC [auth N] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth D] Focus chain UC [auth N] Focus chain UD [auth Q] Focus chain V [auth A] Focus chain VB [auth D] Focus chain VC [auth N] Focus chain VD [auth Q] Focus chain W [auth A] Focus chain WB [auth D] Focus chain WC [auth N] Focus chain WD [auth Q] Focus chain X [auth A] Focus chain XB [auth D] Focus chain XD [auth Q] Focus chain Y [auth A] Focus chain YB [auth D] Focus chain YC [auth O] Focus chain YD [auth Q] Focus chain Z [auth A] Focus chain ZA [auth C] Focus chain ZC [auth O] Focus chain ZD [auth Q]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.223
R-Value Work: 0.184
R-Value Observed: 0.186
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.7	α = 90
b = 200.753	β = 90.06
c = 67.631	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-08-25

Deposition Author(s):

Ruprecht, J.

Iwata, S.

Cecchini, G.

Revision History (Full details and data files)

Version 1.0: 2010-08-25
Type: Initial release
Version 1.1: 2012-04-25
Changes: Database references, Non-polymer description, Other, Version format compliance
Version 1.2: 2015-05-20
Changes: Non-polymer description
Version 1.3: 2019-01-30
Changes: Data collection, Experimental preparation
Version 1.4: 2019-02-06
Changes: Data collection, Experimental preparation
Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Derived calculations, Other, Structure summary
Version 2.0: 2023-12-20
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary